8CPB | pdb_00008cpb

1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with AMPPNP, and AnhMurNAc at 1.7 Angstroms resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QBW	same protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	20% PEG 3350, Na/K tartrate 0.2M

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.67	α = 90
b = 90.67	β = 90
c = 171.686	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2022-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	46.25	100	0.24	0.99	17.4	20.7		87575

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	100		0.398	0.81	1.9	20.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	46.249	87521	4235	99.979	0.171	0.1689	0.18	0.2046	0.21	28.328

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
5.196			5.196		-10.392

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.12
r_dihedral_angle_3_deg	13.747
r_dihedral_angle_1_deg	6.385
r_dihedral_angle_2_deg	5.396
r_lrange_it	3.591
r_lrange_other	3.553
r_scangle_it	2.296
r_scangle_other	2.296
r_mcangle_it	1.964
r_mcangle_other	1.964
r_scbond_it	1.515
r_scbond_other	1.515
r_mcbond_it	1.285
r_mcbond_other	1.284
r_angle_refined_deg	1.071
r_angle_other_deg	0.707
r_nbd_other	0.249
r_nbd_refined	0.213
r_symmetry_nbd_refined	0.203
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.142
r_chiral_restr_other	0.141
r_symmetry_xyhbond_nbd_refined	0.127
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.055
r_bond_other_d	0.017
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5494
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	132

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement